基于转录组测序技术鉴别影响莱芜猪滴水损失的关键基因

doi:10.11843/j.issn.0366-6964.2025.03.015

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (3): 1134-1146.doi: 10.11843/j.issn.0366-6964.2025.03.015

基于转录组测序技术鉴别影响莱芜猪滴水损失的关键基因

贾万里¹^,²(), 王继英², 李菁璇², 王彦平², 耿立英¹, 张传生¹^,*(), 赵雪艳²^,*()

1. 河北科技师范学院动物科技学院, 秦皇岛 066600
2. 山东省农业科学院畜牧兽医研究所, 农业农村部畜禽生物组学重点实验室/山东省畜禽疫病防治与繁育重点实验室, 济南 250100

收稿日期:2024-10-08 出版日期:2025-03-23 发布日期:2025-04-02
通讯作者: 张传生,赵雪艳 E-mail:3311896682@qq.com;cszhang1976@126.com;zhaoxueyan0102@163.com
作者简介:贾万里(1996-)，男，河南驻马店人，硕士生，主要从事猪遗传育种与繁殖研究，E-mail: 3311896682@qq.com
基金资助:
山东省重点研发计划(2022LZGCQY007；2022LZGC003)；山东省生猪产业技术体系(SDAIT-08-03)；山东省自然科学基金(ZR2024MC064)

Identification of Key Genes Affecting Drip Loss in Laiwu Pigs Based on Transcriptome Sequencing Technology

JIA Wanli¹^,²(), WANG Jiying², LI Jingxuan², WANG Yanping², GENG Liying¹, ZHANG Chuansheng¹^,*(), ZHAO Xueyan²^,*()

1. College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600, China
2. Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs/Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China

Received:2024-10-08 Online:2025-03-23 Published:2025-04-02
Contact: ZHANG Chuansheng, ZHAO Xueyan E-mail:3311896682@qq.com;cszhang1976@126.com;zhaoxueyan0102@163.com

摘要/Abstract

摘要：

旨在筛选影响莱芜猪滴水损失的关键基因，以提高猪肉质品质并减少滴水带来的经济损失。本研究选取胴体重为(72.30±1.26) kg的28头莱芜猪(公猪19头，母猪9头)，测定48 h滴水损失、肉色、肌内脂肪含量和pH等肉质性状，并进行背最长肌组织的转录组测序。利用滴水损失极端个体(每组各3头公猪，1头母猪)，在log₂(差异倍数) ≥1且校正后P≤0.01的筛选标准下，筛选差异表达基因。结合差异基因与表型的相关分析和蛋白互作分析进一步鉴别影响莱芜猪滴水损失的关键候选基因。结果发现，莱芜猪滴水损失与肌内脂肪含量以及1 h和24 h肉色a^*值呈显著负相关(P < 0.05)。滴水损失高、低组间共筛选到166个差异表达基因，这些基因显著富集在与血管系统发育与功能、细胞骨架与运动、蛋白质调控与功能等相关的GO条目和通路中。在28个个体中的相关性分析发现，差异表达基因中有110个基因与滴水损失呈显著相关(P < 0.05)，前10位显著相关的差异表达基因包含了KLF2和IGF2等功能上与滴水损失密切相关的基因。进一步的蛋白互作分析发现，差异表达基因中UBR1和TTBK2所表达的蛋白与其它蛋白存在最多的互作，其基因mRNA表达量与滴水损失显著相关(P < 0.05)，且已报道的基因功能也与滴水损失密切相关。因此，结合差异表达基因分析、相关性分析和蛋白互作分析将KLF2、IGF2、UBR1和TTBK2作为影响滴水损失的重要候选基因。本研究为猪滴水损失分子机制的解析奠定基础，也为猪肉质性状改良提供了重要借鉴。

关键词: 莱芜猪, 滴水损失, RNA测序, 肉质性状, 候选基因

Abstract:

This study aimed to identify key genes affecting drip loss in Laiwu pigs to improve pork quality and reduce economic loss caused by drip. Twenty-eight Laiwu pigs, including 19 boars and 9 sows with carcass weight of (72.30±1.26) kg, were selected as experimental animals. The meat quality traits, including 48 h drip loss, meat color, intramuscular fat content, and pH, were measured. RNA sequencing was conducted on the longissimus dorsi muscle tissue of these pigs. Then, differentially expressed genes (DEGs) were detected based on the criteria of log₂(fold change) ≥1 and an adjusted P≤0.01 between groups with high and low drip loss. Each group included three boars and one sow. By combining correlation analysis between DEGs and drip loss, as well as protein-protein interaction (PPI) analysis, the candidate genes influencing drip loss in Laiwu pigs were further identified. The results indicated that drip loss was significantly negatively correlated with the intramuscular fat content and the a^* value of meat color at both 1 h and 24 h post-mortem (P < 0.05) in Laiwu pigs. A total of 166 DEGs were identified between the high and low drip loss groups. These DEGs were significantly enriched in Gene Ontology (GO) terms and pathways related to cardiovascular system development and function, cytoskeleton and motility, and protein regulation and function. Correlation analysis using the 28 individuals revealed that 110 of the 166 DEGs were significantly correlated with drip loss (P < 0.05). Among the top ten of the most significantly correlated DEGs, two genes, KLF2 and IGF2, were identified, whose functions were reported to be related to drip loss. Furthermore, PPI analysis of DEGs identified two proteins, which were encoded by UBR1 and TTBK2, having the highest number of interactions with other proteins, and the mRNA expression levels of the two genes were significantly correlated with drip loss (P < 0.05). These gene functions were also reported closely related to drip loss in previous studies. Therefore, by combining the results of DEG analysis, correlation analysis, and PPI analysis, KLF2, IGF2, UBR1 and TTBK2 were identified as candidate genes affecting drip loss. This study lays the ground for elucidating the molecular mechanisms underlying the drip loss in pigs and offers valuable insights for the improvement of meat quality traits in pigs.

Key words: Laiwu pig, drip loss, RNA sequencing, meat quality traits, candidate genes

中图分类号:

S828.2

贾万里, 王继英, 李菁璇, 王彦平, 耿立英, 张传生, 赵雪艳. 基于转录组测序技术鉴别影响莱芜猪滴水损失的关键基因[J]. 畜牧兽医学报, 2025, 56(3): 1134-1146.

JIA Wanli, WANG Jiying, LI Jingxuan, WANG Yanping, GENG Liying, ZHANG Chuansheng, ZHAO Xueyan. Identification of Key Genes Affecting Drip Loss in Laiwu Pigs Based on Transcriptome Sequencing Technology[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1134-1146.

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性状 Trait	平均值±标准误 Mean±Standard error	中位数 Median	最小值 Minimum value	最大值 Maximum value	变异系数/% Coefficient of variation
胴体重/kg Carcass weight	72.30±1.26	6.64	72.48	60.00	83.10
亮度L1 Lightness L1	43.74±0.60	44.20	38.53	49.75	7.31
红度a1 Redness a1	16.19±0.43	15.97	11.89	20.19	14.02
黄度b1 Yellowness b1	8.95±0.20	8.93	6.73	10.98	11.86
亮度L24 Lightness L24	45.49±0.91	44.73	37.80	60.83	10.60
红度a24 Redness a24	17.62±0.36	17.29	13.72	20.97	10.70
黄度b24 Yellowness b24	9.41±0.24	9.29	7.31	12.03	13.41
1小时pH pH₁_h	6.69±0.05	6.76	6.15	7.18	3.89
24小时pH pH₂₄_h	6.47±0.06	6.47	5.73	6.95	4.61
肌内脂肪含量/% Intramuscular fat content	8.82±0.80	8.10	3.19	18.57	48.20
48小时滴水损失/% 48 h drip loss(DL48h)	1.44±0.14	1.30	0.49	3.97	52.17

项目 Item	平均值 Mean	最小值 Minimum value	最大值 Maximum value	标准差 Standard deviation
原始读段/bp Raw reads	45 781 549.43	41 020 608	51 117 088	442 854.90
去冗余片段/bp Clean reads	44 329 938.71	40 346 978	49 275 354	458 787.63
总比对率/% Total mapping rate	95.13	92.63	96.65	0.19
单一比对率/% Unique mapping rate	92.04	89.71	93.04	0.17
碱基数/G Base count	6.65	6.05	7.39	0.07
碱基质量分值/% (Q20) Base quality score (Q20)	98.04	97.14	98.47	0.07
碱基质量分值/% (Q30) Base quality score (Q30)	94.56	92.50	95.74	0.18

项目 Item	低滴水损失组 DL-L	高滴水损失组 DL-H	P值 P-value
胴体重/kg Carcass weight	65.68±2.02	73.34±3.10	0.091 6
亮度L1 Lightness L1	40.91±1.32	44.86±0.98	0.056 5
红度a1 Redness a1	18.58±0.94	13.78±0.98	0.012 3^*
黄度b1 Yellowness b1	8.69±0.55	8.55±0.18	0.826 6
亮度L24 Lightness L24	46.04±1.70	42.71±3.09	0.391 1
红度a24 Redness a24	19.61±0.60	16.21±0.87	0.021 1^*
黄度b24 Yellowness b24	9.56±0.35	8.84±0.85	0.480 4
1小时pH pH_{1 h}	6.98±0.07	6.78±0.03	0.060 9
24小时pH pH_{24 h}	6.68±0.03	6.63±0.16	0.795 3
肌内脂肪含量/% Intramuscular fat content	11.93±1.90	5.10±0.62	0.031 2^*
48小时滴水损失/% 48 h drip loss(DL48 h)	0.61±0.07	2.88±0.37	0.007 6^**

基因ID Gene ID	基因名称 Gene name	差异倍数 Fold change	P值 P-value	染色体 Chromosome	基因描述 Gene description
ENSSSCG00000011363	PRKAR2A	5.920	1.63×10^-11	13	蛋白激酶c AMP依赖的Ⅱ型调节亚基α protein kinase cAMP-dependent type Ⅱ regulatory subunit alpha
ENSSSCG00000039290	MTPN	5.727	1.55×10^-9	18	肌营养蛋白myotrophin
ENSSSCG00000029558	EXTL1	0.172	3.98×10^-9	6	外泌体样糖基转移酶1 exostosin like glycosyltransferase 1
ENSSSCG00000050398	-	5.607	5.70×10^-9	5	-
ENSSSCG00000004980	THSD4	4.182	6.70×10^-9	1	含血小板反应蛋白1型结构域4 thrombospondin type 1 domain containing 4
ENSSSCG00000030921	APOA1	0.293	8.47×10^-9	9	载脂蛋白A1 apolipoprotein A1
ENSSSCG00000014291	AFF4	4.812	9.87×10^-9	2	AF4/FMR2家族成员4 AF4/FMR2 family member 4
ENSSSCG00000017268	PRKCA	3.909	2.01×10^-8	12	蛋白激酶Cα protein kinase C alpha
ENSSSCG00000017791	-	4.414	2.34×10^-8	12	弹弓蛋白磷酸酶2 slingshot protein phosphatase 2
ENSSSCG00000013598	KANK3	0.296	2.44×10^-8	2	KN基序和锚蛋白重复结构域3 KN motif and ankyrin repeat domains 3

类别 Category	项目 Item	编号 ID	描述 Description	P值 P-value	富集基因个数 Enriched gene count
GO	BP	GO: 0003018	循环系统中的血管过程 vascular process in circulatory system	2.60×10^-5	6
		GO: 0001944	脉管系统发育 vasculature development	2.70×10^-5	14
		GO: 0072358	心血管系统发育 cardiovascular system development	2.70×10^-5	14
	CC	GO: 0001725	应力纤维stress fiber	2.05×10^-3	3
		GO: 0097517	收缩型肌动蛋白丝束 contractile actin filament bundle	2.05×10^-3	3
		GO: 0032432	肌动蛋白丝束 actin filament bundle	2.89×10^-3	3
	MF	GO: 0035173	组蛋白激酶活性 histone kinase activity	3.58×10^-3	2
		GO: 0051393	α-辅肌动蛋白结合 alpha-actinin binding	4.28×10^-3	2
		GO: 0005518	胶原结合 collagen binding	4.71×10^-3	3
KEGG		ssc04371	Apelin信号通路 Apelin signaling pathway	2.30×10^-5	8
		ssc04730	长时程抑制 long-term depression	1.20×10^-4	5
		ssc04921	催产素信号通路 oxytocin signaling pathway	1.47×10^-4	7

基于转录组测序技术鉴别影响莱芜猪滴水损失的关键基因

Identification of Key Genes Affecting Drip Loss in Laiwu Pigs Based on Transcriptome Sequencing Technology

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基因 Gene	相关系数r Correlation coefficient r	相关性P值 Correlation P-value	差异倍数 Fold change	P值 P-value
RBPMS2	-0.656	1.50×10^-4	0.327	5.56×10^-5
KLF2	-0.586	1.04×10^-3	0.373	5.44×10^-5
IGF2	-0.583	1.13×10^-3	0.388	1.89×10^-5
EDRF1	0.583	1.14×10^-3	2.481	1.08×10^-4
DDIT4	-0.574	1.42×10^-3	0.323	5.44×10^-6
GATA2	-0.573	1.45×10^-3	0.353	1.14×10^-4
ENSSSCG00000001341	-0.570	1.54×10^-3	0.384	3.25×10^-6
RHOBTB2	0.570	1.55×10^-3	3.563	1.88×10^-5
TCP11L1	0.568	1.62×10^-3	2.472	1.11×10^-4
ID3	-0.560	1.97×10^-3	0.330	3.55×10^-7

蛋白名称 Protein name	互作程度 Degree	相关系数r Correlation coefficient	相关P值 Correlation P-value	差异倍数 Fold change	差异P值 P-value	基因描述 Gene description
UBR1	3	0.446	1.734×10^-2	2.749	1.021×10^-4	泛素蛋白连接酶E3组分n-识别蛋白1 ubiquitin protein ligase E3 component n-recognin 1
TTBK2	3	0.408	3.118×10^-2	2.681	8.160×10^-5	Tau微管蛋白激酶2 tau tubulin kinase 2
GATA2	2	-0.573	1.447×10^-3	0.353	1.139×10^-4	GATA结合蛋白2 GATA binding protein 2
PDLIM4	2	-0.525	4.121×10^-3	0.359	9.710×10^-5	PDZ和LIM结构域4 PDZ and LIM domain 4
SPG11	2	0.517	4.811×10^-3	2.510	1.033×10^-4	SPG11囊泡转运相关蛋白, Spatacsin SPG11 vesicle trafficking associated, spatacsin
ATMIN	2	0.509	5.704×10^-3	2.412	9.030×10^-5	ATM相互作用蛋白ATM interactor
CHUK	2	0.488	8.443×10^-3	2.679	3.470×10^-5	核因子κB激酶复合物抑制组分 component of inhibitor of nuclear factor kappa B kinase complex
USP24	2	0.425	2.417×10^-2	2.580	8.300×10^-5	泛素特异性肽酶24 ubiquitin specific peptidase 24
ARHGAP35	2	0.396	3.691×10^-2	2.436	5.240×10^-6	Rho GTPase激活蛋白35 Rho GTPase activating protein 35

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